Maintained by Robin Tecon, microbiologist and postdoctoral researcher at the Swiss Federal Institute of Technology Zürich. This blog is about bacteria (and other microbes) and the scientists who study them.

Pages

Thursday, October 04, 2012

The tree of life versus the rhizome of life

The metaphor of the tree of life—which illustrates the common
descent of all life on Earth—was popularized by Darwin in its Origin of species and later by his
contemporary Haeckel, but apparently its roots can be traced back as early as
the 18th century in the writings of various authors (Archibald,2009). On a different line, it also of course echoes the biblical tree of life
mentioned in the Genesis.

However, about a decade ago, authors such as W. FordDoolittle (1999) have cast doubt on the tree as a valid representation of the history
of living organisms. Since then, articles that question
the tree of life have flourished1. And the debate is far from being
settled.

A tree or a rhizome?

Based on the recent development of comparative genomics, the
microbiologist Didier Raoult suggested in the journal the Lancet that Darwin’s tree of life should be replaced by a rhizome of life (Raoult, 2010). Raoult
sees the rhizome – a complex net of interconnected roots – as a more faithful representation
of the history of living organisms.

What are Raoult’s arguments? We find, first, the understanding
that lateral gene transfer is an essential motor of evolution. Secondly, and it
derives from the first observation, the impossibility to draw a unique phylogenetic
tree for all the genes in one organism; gene-trees disagree with each other. Finally,
we can observe the creation of new genes that don’t belong to any phylogenetic
tree. Raoult writes:

“A
post-Darwinist concept of the living species can be proposed, to integrate the
theories of multiplicity and de-novo creation. In accordance with the theory on
the evolution of human societies proposed by Deleuze and Guattari, I believe
that the evolution of species looks much more like a rhizome (or a mycelium)
[…]. Consequently, this view of evolution resembles a clump of roots that
considers the occurrence of multiplicities.”

I think that Raoult’s proposition is at the same time a very
interesting idea and a very bad idea.

Now it is true that our view of the evolution of bacteria
has changed profoundly since we know that lateral (horizontal) gene transfer is
a very important process that shapes bacterial genomes. Does it apply to
eukaryotes? For sure important gene transfers have occurred (endosymbiosis of
mitochondria and chloroplasts, for instance), but during most historical time
it probably remained a side phenomenon in eukaryotes. Hence, I don’t see how it
could invalidate the tree of life concept.

The multiplicity of phylogenetic trees that can be drawn for
each gene in one organism is another interesting problem raised by Raoult.
Eugene Koonin, in his book The logic of chance, notes the incongruence between gene-trees in one given organism. But
interestingly he writes (p.165):

“However, notwithstanding the newly discovered web-like
character of evolution, Darwin’s metaphor reflects a deeper truth: Trees remain
the natural representation of the histories of individual genes, given the
fundamentally bifurcating character of gene replication and the substantially
low frequency of intragenic recombination compared to intergenic recombination
at long evolutionary distances”

Koonin further suggests to replace the tree of life by a forest of life, a collection of all
gene-trees. I think both the rhizome and
the forest are unnecessary complications. After all, the tree of life doesn’t have
to be reduced to a phylogenetic tree. If we speak of the tree of life as a
model, it still stands very well (as Koonin emphasizes, there is something
intrinsically “tree-like” in the evolutionary process). And a model is not the
exact depiction of reality (or it wouldn’t be a model anymore!) .

As to the last argument of Raoult – the de novo formation of genes –, I simply don’t understand what he
means, since present genes have all evolved from ancestor genes!

Maybe more important: when we compare the merits of the tree
and the rhizome as a metaphor for the history of life, the tree wins flat out. One
great achievement of the tree of life was to illustrate how all creatures
originated through common descent and variation, therefore undermining the
belief in the immutability of species (the creationist view). It is difficult
to find another image that would strike the mind with such beauty and power.
Sorry, but most non-scientists don’t know what a rhizome is in the first place!
If we were to exchange the tree metaphor for the rhizome, I believe we would
muddle up things, not clarify them.

Promoting the rhizome

But the battle still rages on. The open-access journal Frontiers has a new collection
(“Research topic”) edited by Didier Raoult and Eugene Koonin, which is mostly dedicated
to the defense of the rhizome of life concept.(Curiously it was published in Frontiers
in cellular and infection microbiology, not in its sister journal Frontiers in evolutionary and population
genetics).

The collection consists of fourteen articles (five of which are co-authored
by Raoult, one by Koonin), and its provocative title is “Microbial genomics challengeDarwin” (awful title in my opinion; I explain why later). I didn’t read
everything (far from it), but basically they discuss how modern knowledge
undermines the “dogma” of Darwinism, and thus they ask for a “post-modern”
theory of evolution seen as a “paradigm shift”. The editors write, in their
editorial, that “pervasive horizontal gene transfer makes the original concept
of the Tree of Life largely obsolete.”

“Natural selection is not an “evolutionary force” but the
necessary outcome of variation and multiplication. In particular, natural
selection cannot be weakened by mechanisms that promote variations (such as
epigenetic mechanisms or symbiogenesis), because these processes provide more
substrates for selection.”

Leave the old man in peace!

Now something makes me wince, and that is the recent habit
to attack Darwin, whenever evolution is discussed, as if he were a present-day
scientist. What is the point? It is not as if the theory of evolution had been
frozen since Darwin; the great man didn’t even know of genes! What these
attackers really challenge in their
writings is most often modern synthesis (neo-darwinism), not the view of
Charles Darwin. Forterre expresses this very clearly:

“This is a sensitive topic, considering the renewal of
creationist thinking in fundamentalist religious circles and the wide publicity
given to these “non-orthodox views.” This was best illustrated by the cover of
the “New Scientists” issue published in January 2009 showing a tree of
life superimposed with the sentence: “Darwin was wrong.” Although the
existence of anti-Darwinists in the political arena is certainly not a reason
to hide fierce debates between evolutionists over mechanisms and
representations of evolution, one can regret to see the name of Darwin used as
a foil in these debates. After all, nobody said: “Mendel was wrong”
because his concept of the gene was quite different from what we know today
(personal quote from Eduardo Rocha).”

And as part of his conclusion:

“At the dawn of the XXI century, some biologists apparently
dream to bypass Darwin. For me, this is hopeless, except if we reduce Darwin to
some ad hoc version of « Darwinism » or if we consider Darwin as one of
our contemporaries, and not a scientist of the XIX century. With the dyad
variation/selection, Darwin has provided us with key concepts that are
necessary and sufficient to understand the logic of evolution, a goldmine that
is still open. All the striking discoveries made in biology during the last 150
years have been extensions of these concepts and recent discoveries in
microbial evolution and post-genomic studies are not different.”

Indeed, attacks on Darwin do not come in short supply in “Microbial
genomics challenge Darwin”. In the presentation of the research topic by the
editors:

“The 200th anniversary of Darwin’s birthday was celebrated
in 2009, making the concept of Darwinism even more popular than at the time it
was originally proposed, to the extent that it has acquired quasi-religious
status.”

We certainly don’t share the same definition of religion. Darwin a prophet? What did I know!

Today’s research on microbial genomics reveals amazing new
facts, and it’s important that we discuss how they modify our current knowledge
on evolution. But this should be no excuse for a fake controversy with a
scientist who died one hundred thirty years ago.

Once more, Patrick Forterre has written exactly the right words:

“whatsoever Darwin’s limitations, I will argue that we still
have more to gain standing on his shoulder than tripping him, especially when
he cannot reply.”

1 comment:

he can not reply , but a lot of dogmatic defenders talk in his name. Since his times, when he had the support of the X-club until today when exists a lot of dogmatic defenders. All refuse to see the obvious reality of the utter weakness of the theory of natural selection (one hundred tautology taken from previous authors) as it does not explain the transfomacion of species. It is purely a semantic game, empty reasoning, it comes down to that all that exists was created by this "force, process, mechanism, differential reproduction, result of differential reproduction, and so on." . An overpowering force and a lot of uncritical acolytes. Here we have the religion.

(creationism, an enemy to the level of Darwinism, was created and sustained by Darwinists to argue with a religion and never scientifically with its own fallacies)